Mitochondria analytics
Visualization and analysis tools for analyzing mitochondria in the Layer 2/3 EM volume
visualize all mitochondria in a cell of interest
Contents
Folders
classifier
folder: mitochondria classifier using random forests for pyramidal
neurons in the Layer 2/3 volume.
mito_to_mito_distance_statistics
folder: summary statistics for mitochondria-to-mitochondria (mito
centroid-to-mito centroid) used in the classifier analysis.
node_metrics
folder: derivation of mitochondria segmentation node metrics
(“nodeplots”).
Visualization tools
Visualize a single mitochondrion of interest in Neuroglancer
neuroglancer_link_generator_mitochondria_visualization_version.ipynb:
generate a Neuroglancer link for a single cellid and single
mitochondrion from the
pni_mito_cellswskel_v185_fullstats.csv datatable. The view
will be centered at the centroid of the mitochondrion in the volume.
neuroglancer link to a single mitochondrion with crosshair at the mito centroid
Visualize all mitochondria in a neuron of interest in Neuroglancer
neuroglancer_link_generator_all_mitochondria.ipynb:
generate a Neuroglancer link for all the mitochondria in a single cellid
of interest pulling the mito ids from the
211019_mitochondria_info.csv datatable.
neuroglancer link generator for all mitochondria in a cell
Visualize neuronal mitochondria by compartment in Neuroglancer
neuroglancer_link_generator_neuronalmitochondria_bycompartment.ipynb:
as above, but allows to select for a compartment of interest. Neuronal
compartment assignments are based on the method described by
Reconstruction of neocortex: Organelles, compartments, cells,
circuits, and activity Turner
et al, Cell 2022.
neuroglancer link generator for mitochondria by compartment
3D visualizer of all mitochondria in a cell of interesting using Meshparty, vtk, and OpenGL viewer
vtk_mitochondria_visualizer.ipynb:
generate a 3D interactive view of all mitochondria in a cell of
interest. Note this method has significant file download and space
requirements compared to using the Neuroglancer viewer.
3D visualizer of all mitochondria in a cell
vtk_pyr_mitochondria_visualizer_bycompartment_with_neuroglancer_all_mitos.ipynb:
As above but colors mitochondria by compartment (as reported by Turner
et. al., Cell 2022).
